Clarifications on tensions.traj and forces.traj outputs

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MEDYAN

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Aug 17, 2020, 3:01:22 PM8/17/20
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Here I hope to clarify the two outputs files: tensions.traj and forces.traj. 

The tensions.traj records the axial force on each filament cylinder, motor and linker. It is positive if the force is tensile, or negative if the force is compressive

The forces.traj records the total force (bending + stretching + steric + ...) on each filament beads, motor, linker, etc. after mechanical minimization. This output is normally used for benchmarking mechanical minimization. In MEDYAN, the minimization protocol will be carried out until the force is smaller than the threshold (GRADIENTTOLERANCE) everywhere. After a successful minimization, we expect this force to be small (< or ~ 1pN) for all elements. 


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